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### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:wateRmelon.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings wateRmelon_2.8.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/wateRmelon.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘wateRmelon/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘wateRmelon’ version ‘2.8.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
'Biobase', 'limma', 'matrixStats', 'methylumi', 'lumi', 'ROC',
'IlluminaHumanMethylation450kanno.ilmn12.hg19', 'illuminaio'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘wateRmelon’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
‘Biobase’
A package should be listed in only one of these fields.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Packages in Depends field not imported from:
‘IlluminaHumanMethylation450kanno.ilmn12.hg19’ ‘matrixStats’
‘methylumi’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
Unexported objects imported by ':::' calls:
‘minfi:::.annoGet’ ‘minfi:::.availableAnnotation’
‘minfi:::.isRGOrStop’
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.adjusted_normalizeFunnorm450k : unbiased_normalizeQuantiles: no
visible global function definition for ‘colQuantiles’
.adjusted_normalizeFunnorm450k: no visible global function definition
for ‘getMeth’
.adjusted_normalizeFunnorm450k: no visible global function definition
for ‘getUnmeth’
.adjusted_normalizeFunnorm450k: no visible global function definition
for ‘assay<-’
.buildControlMatrix450k: no visible global function definition for
‘colMeans2’
.extractFromRGSet450k: no visible global function definition for
‘getProbeInfo’
.extractFromRGSet450k: no visible global function definition for
‘getRed’
.extractFromRGSet450k: no visible global function definition for
‘getGreen’
.extractFromRGSet450k: no visible global function definition for
‘getOOB’
.extractFromRGSet450k: no visible global function definition for
‘colQuantiles’
.getFunnormIndices: no visible global function definition for
‘getProbeType’
.getFunnormIndices: no visible global function definition for
‘seqnames’
.isMatrixBacked: no visible global function definition for ‘assays’
.regularizeQuantiles: no visible global function definition for
‘colCummaxs’
.returnFit: no visible global function definition for ‘rowMeans2’
IDATsToMatrices2: no visible global function definition for ‘.mclapply’
NChannelSetToMethyLumiSet2: no visible global function definition for
‘betas’
NChannelSetToMethyLumiSet2: no visible global function definition for
‘methylated’
NChannelSetToMethyLumiSet2: no visible global function definition for
‘unmethylated’
NChannelSetToMethyLumiSet2: no visible global function definition for
‘pval.detect<-’
adjustedFunnorm: no visible global function definition for
‘preprocessNoob’
adjustedFunnorm: no visible global function definition for
‘mapToGenome’
adjustedFunnorm: no visible global function definition for ‘addSex’
adjustedFunnorm: no visible global function definition for ‘getSex’
adjustedFunnorm: no visible global function definition for ‘getCN’
adjustedFunnorm: no visible global function definition for ‘assay<-’
beadcount: no visible global function definition for ‘getNBeads’
beadcount: no visible global function definition for ‘getProbeInfo’
beadcount: no visible global function definition for ‘getManifestInfo’
bgIntensitySwan.methylumi: no visible global function definition for
‘colMedians’
bscon_methy: no visible global function definition for
‘intensitiesByChannel’
bscon_methy: no visible global function definition for ‘QCdata’
bscon_minfi : csp.green: no visible global function definition for
‘getRed’
bscon_minfi : csp.green: no visible global function definition for
‘getGreen’
bscon_minfi : csp.green : <anonymous>: no visible global function
definition for ‘getControlAddress’
bscon_minfi : csp.red: no visible global function definition for
‘getRed’
bscon_minfi : csp.red: no visible global function definition for
‘getGreen’
bscon_minfi : csp.red : <anonymous>: no visible global function
definition for ‘getControlAddress’
combo : <anonymous>: no visible global function definition for ‘QCdata’
combo: no visible global function definition for ‘QCdata<-’
dfort: no visible binding for global variable
‘IlluminaHumanMethylation450kanno.ilmn12.hg19’
epicv2clean.gds.class: no visible global function definition for
‘chainsaw’
estimateSex: no visible global function definition for ‘head’
estimateSex: no visible binding for global variable ‘sex_coef’
estimateSex: no visible global function definition for ‘colSds’
genall: no visible global function definition for ‘head’
generateManifest: no visible global function definition for
‘getAnnotationObject’
generateManifest: no visible global function definition for
‘getAnnotation’
generateManifest: no visible global function definition for
‘getProbeInfo’
getMethylationBeadMappers2 : <anonymous>: no visible binding for global
variable ‘hm27.ordering’
getMethylationBeadMappers2 : <anonymous>: no visible binding for global
variable ‘hm450.ordering’
getMethylationBeadMappers2 : <anonymous>: no visible binding for '<<-'
assignment to ‘epic.ordering’
getMethylationBeadMappers2 : <anonymous>: no visible binding for global
variable ‘epic.ordering’
getMethylationBeadMappers2 : <anonymous>: no visible binding for '<<-'
assignment to ‘epicV2.ordering’
getMethylationBeadMappers2 : <anonymous>: no visible binding for global
variable ‘epicV2.ordering’
getMethylationBeadMappers2 : <anonymous>: no visible binding for global
variable ‘hm27.controls’
getMethylationBeadMappers2 : <anonymous>: no visible binding for global
variable ‘hm450.controls’
getMethylationBeadMappers2 : <anonymous>: no visible binding for global
variable ‘epic.controls’
getMethylationBeadMappers2 : <anonymous>: no visible binding for global
variable ‘epicV2.controls’
getMethylumiBeta: no visible global function definition for
‘unmethylated’
getMethylumiBeta: no visible global function definition for
‘methylated’
got: no visible global function definition for ‘getProbeInfo’
lumiMethyR2: no visible global function definition for ‘methylumiR’
oxyscale: no visible global function definition for ‘betas’
oxyscale: no visible global function definition for ‘betas<-’
p_dfsfit: no visible global function definition for ‘mclapply’
pipelineIlluminaMethylation.batch: no visible binding for global
variable ‘PATH_RES’
pipelineIlluminaMethylation.batch: no visible binding for global
variable ‘probeAnnotationsCategory’
preprocessIlluminaMethylation: no visible binding for global variable
‘projectName’
readEPIC: no visible binding for global variable ‘n.sd’
uSexQNengine: no visible global function definition for ‘mclapply’
BMIQ,MethyLumiSet : <anonymous>: no visible global function definition
for ‘warn’
BMIQ,MethyLumiSet: no visible global function definition for ‘betas<-’
BMIQ,MethylSet: no visible global function definition for ‘getBeta’
BMIQ,MethylSet : <anonymous>: no visible global function definition for
‘warn’
adjustedDasen,MethyLumiSet: no visible global function definition for
‘methylated’
adjustedDasen,MethyLumiSet: no visible global function definition for
‘unmethylated’
adjustedDasen,MethyLumiSet: no visible global function definition for
‘betas<-’
adjustedDasen,MethyLumiSet: no visible global function definition for
‘methylated<-’
adjustedDasen,MethyLumiSet: no visible global function definition for
‘unmethylated<-’
adjustedDasen,MethylSet: no visible global function definition for
‘getMeth’
adjustedDasen,MethylSet: no visible global function definition for
‘getUnmeth’
adjustedDasen,MethylSet: no visible global function definition for
‘getAnnotation’
adjustedDasen,MethylSet: no visible global function definition for
‘MethylSet’
adjustedDasen,MethylSet: no visible global function definition for
‘colData’
adjustedDasen,MethylSet: no visible global function definition for
‘metadata’
adjustedDasen,RGChannelSet: no visible global function definition for
‘preprocessRaw’
agep,MethylSet: no visible global function definition for ‘getBeta’
as.methylumi,MethyLumiSet: no visible global function definition for
‘methylated’
as.methylumi,MethyLumiSet: no visible global function definition for
‘unmethylated’
as.methylumi,MethyLumiSet: no visible global function definition for
‘betas’
as.methylumi,MethyLumiSet: no visible global function definition for
‘pvals’
as.methylumi,MethyLumiSet: no visible global function definition for
‘QCdata’
as.methylumi,MethylSet: no visible global function definition for
‘getMeth’
as.methylumi,MethylSet: no visible global function definition for
‘getUnmeth’
as.methylumi,MethylSet: no visible global function definition for
‘getBeta’
as.methylumi,MethylSet: no visible global function definition for
‘getAnnotation’
betaqn,MethyLumiSet: no visible global function definition for
‘betas<-’
betaqn,MethyLumiSet: no visible global function definition for ‘betas’
betaqn,MethylSet: no visible global function definition for ‘getBeta’
betaqn,RGChannelSet: no visible global function definition for
‘getBeta’
colnames,MethyLumiSet: no visible global function definition for
‘methylated’
danen,MethyLumiSet: no visible global function definition for
‘methylated’
danen,MethyLumiSet: no visible global function definition for
‘unmethylated’
danen,MethyLumiSet: no visible global function definition for ‘betas<-’
danen,MethyLumiSet: no visible global function definition for
‘methylated<-’
danen,MethyLumiSet: no visible global function definition for
‘unmethylated<-’
danen,MethylSet: no visible global function definition for ‘getMeth’
danen,MethylSet: no visible global function definition for ‘getUnmeth’
danen,MethylSet: no visible global function definition for ‘MethylSet’
danen,MethylSet: no visible global function definition for ‘colData’
danen,MethylSet: no visible global function definition for ‘metadata’
danen,RGChannelSet: no visible global function definition for
‘preprocessRaw’
danes,MethyLumiSet: no visible global function definition for
‘methylated’
danes,MethyLumiSet: no visible global function definition for
‘unmethylated’
danes,MethyLumiSet: no visible global function definition for ‘betas<-’
danes,MethyLumiSet: no visible global function definition for
‘methylated<-’
danes,MethyLumiSet: no visible global function definition for
‘unmethylated<-’
danes,MethylSet: no visible global function definition for ‘getMeth’
danes,MethylSet: no visible global function definition for ‘getUnmeth’
danes,MethylSet: no visible global function definition for ‘MethylSet’
danes,MethylSet: no visible global function definition for ‘colData’
danes,MethylSet: no visible global function definition for ‘metadata’
danes,RGChannelSet: no visible global function definition for
‘preprocessRaw’
danet,MethyLumiSet: no visible global function definition for
‘methylated’
danet,MethyLumiSet: no visible global function definition for
‘unmethylated’
danet,MethyLumiSet: no visible global function definition for ‘betas<-’
danet,MethyLumiSet: no visible global function definition for
‘methylated<-’
danet,MethyLumiSet: no visible global function definition for
‘unmethylated<-’
danet,MethylSet: no visible global function definition for ‘getMeth’
danet,MethylSet: no visible global function definition for ‘getUnmeth’
danet,MethylSet: no visible global function definition for ‘MethylSet’
danet,MethylSet: no visible global function definition for ‘colData’
danet,MethylSet: no visible global function definition for ‘metadata’
danet,RGChannelSet: no visible global function definition for
‘preprocessRaw’
dasen,MethyLumiSet: no visible global function definition for
‘methylated’
dasen,MethyLumiSet: no visible global function definition for
‘unmethylated’
dasen,MethyLumiSet: no visible global function definition for ‘betas<-’
dasen,MethyLumiSet: no visible global function definition for
‘methylated<-’
dasen,MethyLumiSet: no visible global function definition for
‘unmethylated<-’
dasen,MethylSet: no visible global function definition for ‘getMeth’
dasen,MethylSet: no visible global function definition for ‘getUnmeth’
dasen,MethylSet: no visible global function definition for ‘MethylSet’
dasen,MethylSet: no visible global function definition for ‘colData’
dasen,MethylSet: no visible global function definition for ‘metadata’
dasen,RGChannelSet: no visible global function definition for
‘preprocessRaw’
daten1,MethyLumiSet: no visible global function definition for
‘methylated’
daten1,MethyLumiSet: no visible global function definition for
‘unmethylated’
daten1,MethyLumiSet: no visible global function definition for
‘betas<-’
daten1,MethyLumiSet: no visible global function definition for
‘methylated<-’
daten1,MethyLumiSet: no visible global function definition for
‘unmethylated<-’
daten1,MethylSet: no visible global function definition for ‘getMeth’
daten1,MethylSet: no visible global function definition for ‘getUnmeth’
daten1,MethylSet: no visible global function definition for ‘MethylSet’
daten1,MethylSet: no visible global function definition for ‘colData’
daten1,MethylSet: no visible global function definition for ‘metadata’
daten1,RGChannelSet: no visible global function definition for
‘preprocessRaw’
daten2,MethyLumiSet: no visible global function definition for
‘methylated’
daten2,MethyLumiSet: no visible global function definition for
‘unmethylated’
daten2,MethyLumiSet: no visible global function definition for
‘betas<-’
daten2,MethyLumiSet: no visible global function definition for
‘methylated<-’
daten2,MethyLumiSet: no visible global function definition for
‘unmethylated<-’
daten2,MethylSet: no visible global function definition for ‘getMeth’
daten2,MethylSet: no visible global function definition for ‘getUnmeth’
daten2,MethylSet: no visible global function definition for ‘MethylSet’
daten2,MethylSet: no visible global function definition for ‘colData’
daten2,MethylSet: no visible global function definition for ‘metadata’
daten2,RGChannelSet: no visible global function definition for
‘preprocessRaw’
dmrse,MethylSet: no visible global function definition for ‘getBeta’
dmrse,MethylSet: no visible global function definition for ‘head’
dmrse,RGChannelSet: no visible global function definition for ‘getBeta’
dmrse,RGChannelSet: no visible global function definition for ‘head’
dmrse_col,MethylSet: no visible global function definition for
‘getBeta’
dmrse_col,MethylSet: no visible global function definition for ‘head’
dmrse_col,RGChannelSet: no visible global function definition for
‘getBeta’
dmrse_col,RGChannelSet: no visible global function definition for
‘head’
dmrse_row,MethylSet: no visible global function definition for
‘getBeta’
dmrse_row,MethylSet: no visible global function definition for ‘head’
dmrse_row,RGChannelSet: no visible global function definition for
‘getBeta’
dmrse_row,RGChannelSet: no visible global function definition for
‘head’
estimateCellCounts.wateRmelon,MethylSet: no visible global function
definition for ‘getManifest’
estimateCellCounts.wateRmelon,MethylSet: no visible global function
definition for ‘getMeth’
estimateCellCounts.wateRmelon,MethylSet: no visible global function
definition for ‘getUnmeth’
estimateCellCounts.wateRmelon,MethylSet: no visible global function
definition for ‘getBeta’
estimateCellCounts.wateRmelon,RGChannelSet: no visible global function
definition for ‘getManifest’
estimateCellCounts.wateRmelon,RGChannelSet: no visible global function
definition for ‘preprocessRaw’
estimateCellCounts.wateRmelon,RGChannelSet: no visible global function
definition for ‘getMeth’
estimateCellCounts.wateRmelon,RGChannelSet: no visible global function
definition for ‘getUnmeth’
estimateCellCounts.wateRmelon,RGChannelSet: no visible global function
definition for ‘getBeta’
fuks,MethyLumiSet: no visible global function definition for ‘betas<-’
fuks,MethyLumiSet: no visible global function definition for ‘betas’
fuks,MethylSet: no visible global function definition for ‘getBeta’
fuks,RGChannelSet: no visible global function definition for
‘preprocessRaw’
fuks,RGChannelSet: no visible global function definition for ‘getBeta’
genki,MethyLumiSet: no visible global function definition for ‘betas’
genki,MethylSet: no visible global function definition for ‘getBeta’
genki,RGChannelSet: no visible global function definition for
‘getSnpBeta’
nanes,MethyLumiSet: no visible global function definition for
‘methylated’
nanes,MethyLumiSet: no visible global function definition for
‘unmethylated’
nanes,MethyLumiSet: no visible global function definition for ‘betas<-’
nanes,MethyLumiSet: no visible global function definition for
‘methylated<-’
nanes,MethyLumiSet: no visible global function definition for
‘unmethylated<-’
nanes,MethylSet: no visible global function definition for ‘getMeth’
nanes,MethylSet: no visible global function definition for ‘getUnmeth’
nanes,MethylSet: no visible global function definition for ‘MethylSet’
nanes,MethylSet: no visible global function definition for ‘colData’
nanes,MethylSet: no visible global function definition for ‘metadata’
nanes,RGChannelSet: no visible global function definition for
‘preprocessRaw’
nanet,MethyLumiSet: no visible global function definition for
‘methylated’
nanet,MethyLumiSet: no visible global function definition for
‘unmethylated’
nanet,MethyLumiSet: no visible global function definition for ‘betas<-’
nanet,MethyLumiSet: no visible global function definition for
‘methylated<-’
nanet,MethyLumiSet: no visible global function definition for
‘unmethylated<-’
nanet,MethylSet: no visible global function definition for ‘getMeth’
nanet,MethylSet: no visible global function definition for ‘getUnmeth’
nanet,MethylSet: no visible global function definition for ‘MethylSet’
nanet,MethylSet: no visible global function definition for ‘colData’
nanet,MethylSet: no visible global function definition for ‘metadata’
nanet,RGChannelSet: no visible global function definition for
‘preprocessRaw’
nasen,MethyLumiSet: no visible global function definition for
‘methylated’
nasen,MethyLumiSet: no visible global function definition for
‘unmethylated’
nasen,MethyLumiSet: no visible global function definition for ‘betas<-’
nasen,MethyLumiSet: no visible global function definition for
‘methylated<-’
nasen,MethyLumiSet: no visible global function definition for
‘unmethylated<-’
nasen,MethylSet: no visible global function definition for ‘getMeth’
nasen,MethylSet: no visible global function definition for ‘getUnmeth’
nasen,MethylSet: no visible global function definition for ‘MethylSet’
nasen,MethylSet: no visible global function definition for ‘colData’
nasen,MethylSet: no visible global function definition for ‘metadata’
nasen,RGChannelSet: no visible global function definition for
‘preprocessRaw’
naten,MethyLumiSet: no visible global function definition for
‘methylated’
naten,MethyLumiSet: no visible global function definition for
‘unmethylated’
naten,MethyLumiSet: no visible global function definition for ‘betas<-’
naten,MethyLumiSet: no visible global function definition for
‘methylated<-’
naten,MethyLumiSet: no visible global function definition for
‘unmethylated<-’
naten,MethylSet: no visible global function definition for ‘getMeth’
naten,MethylSet: no visible global function definition for ‘getUnmeth’
naten,MethylSet: no visible global function definition for ‘MethylSet’
naten,MethylSet: no visible global function definition for ‘colData’
naten,MethylSet: no visible global function definition for ‘metadata’
naten,RGChannelSet: no visible global function definition for
‘preprocessRaw’
outlyx,MethyLumiSet: no visible global function definition for ‘betas’
outlyx,MethylSet: no visible global function definition for ‘getBeta’
outlyx,RGChannelSet: no visible global function definition for
‘getBeta’
pfilter,MethyLumiSet: no visible global function definition for ‘betas’
pfilter,MethyLumiSet: no visible global function definition for
‘methylated’
pfilter,MethyLumiSet: no visible global function definition for
‘unmethylated’
pfilter,MethyLumiSet: no visible global function definition for ‘pvals’
pfilter,RGChannelSetExtended: no visible binding for global variable
‘RGChannelSetExtended’
pfilter,RGChannelSetExtended: no visible global function definition for
‘preprocessRaw’
pfilter,RGChannelSetExtended: no visible global function definition for
‘detectionP’
pfilter,RGChannelSetExtended: no visible global function definition for
‘subsetByLoci’
pwod,MethyLumiSet: no visible global function definition for ‘betas’
pwod,MethyLumiSet: no visible global function definition for ‘betas<-’
pwod,MethylSet: no visible global function definition for ‘getBeta’
pwod,RGChannelSet: no visible global function definition for ‘getBeta’
seabi,MethyLumiSet: no visible global function definition for ‘betas’
seabi,MethylSet: no visible global function definition for ‘getBeta’
seabi,RGChannelSet: no visible global function definition for ‘getBeta’
swan,MethyLumiSet: no visible global function definition for
‘methylated’
swan,MethyLumiSet: no visible global function definition for
‘unmethylated’
swan,MethyLumiSet: no visible global function definition for
‘intensitiesByChannel’
swan,MethyLumiSet: no visible global function definition for ‘QCdata’
swan,MethyLumiSet: no visible global function definition for ‘getBeta’
swan,MethyLumiSet: no visible global function definition for ‘getMeth’
swan,MethyLumiSet: no visible global function definition for
‘getUnmeth’
swan,MethyLumiSet: no visible global function definition for ‘betas’
swan,RGChannelSet: no visible global function definition for
‘preprocessSWAN’
tost,MethyLumiSet: no visible global function definition for
‘methylated’
tost,MethyLumiSet: no visible global function definition for ‘betas<-’
tost,MethyLumiSet: no visible global function definition for
‘unmethylated’
tost,MethyLumiSet: no visible global function definition for ‘pvals’
tost,RGChannelSet: no visible global function definition for
‘detectionP’
tost,RGChannelSet: no visible global function definition for
‘preprocessRaw’
tost,RGChannelSet: no visible global function definition for ‘getMeth’
tost,RGChannelSet: no visible global function definition for
‘getUnmeth’
uSexQN,MethyLumiSet: no visible global function definition for
‘methylated’
uSexQN,MethyLumiSet: no visible global function definition for
‘unmethylated’
uSexQN,MethyLumiSet: no visible global function definition for
‘betas<-’
uSexQN,MethyLumiSet: no visible global function definition for
‘methylated<-’
uSexQN,MethyLumiSet: no visible global function definition for
‘unmethylated<-’
uSexQN,MethylSet: no visible global function definition for ‘getMeth’
uSexQN,MethylSet: no visible global function definition for ‘getUnmeth’
uSexQN,MethylSet: no visible global function definition for
‘getAnnotation’
uSexQN,MethylSet: no visible global function definition for ‘MethylSet’
uSexQN,MethylSet: no visible global function definition for ‘colData’
uSexQN,MethylSet: no visible global function definition for ‘metadata’
uSexQN,RGChannelSet: no visible global function definition for
‘preprocessRaw’
Undefined global functions or variables:
.mclapply IlluminaHumanMethylation450kanno.ilmn12.hg19 MethylSet
PATH_RES QCdata QCdata<- RGChannelSetExtended addSex assay<- assays
betas betas<- chainsaw colCummaxs colData colMeans2 colMedians
colQuantiles colSds detectionP epic.controls epic.ordering
epicV2.controls epicV2.ordering getAnnotation getAnnotationObject
getBeta getCN getControlAddress getGreen getManifest getManifestInfo
getMeth getNBeads getOOB getProbeInfo getProbeType getRed getSex
getSnpBeta getUnmeth head hm27.controls hm27.ordering hm450.controls
hm450.ordering intensitiesByChannel mapToGenome mclapply metadata
methylated methylated<- methylumiR n.sd preprocessNoob preprocessRaw
preprocessSWAN probeAnnotationsCategory projectName pval.detect<-
pvals rowMeans2 seqnames sex_coef subsetByLoci unmethylated
unmethylated<- warn
Consider adding
importFrom("utils", "head")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... WARNING
Rd files with duplicated alias 'fot':
‘dot-getManifestString.Rd’ ‘got.Rd’
Rd files with duplicated alias 'got':
‘dot-getManifestString.Rd’ ‘got.Rd’
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
‘epicv2clean’ ‘epicv2clean.default’ ‘epicv2clean.gds.class’
Undocumented data sets:
‘sex_coef’
Undocumented S4 methods:
generic 'adjustedDasen' and siglist 'MethyLumiSet'
generic 'adjustedDasen' and siglist 'MethylSet'
generic 'adjustedDasen' and siglist 'RGChannelSet'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object '.getManifestString'
‘annotation’
Documented arguments not in \usage in documentation object '.getManifestString':
‘x’ ‘obj’ ‘fd’ ‘rn’
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
adjustedDasen 30.881 0.933 32.443
sextest 7.703 0.184 8.155
seabi 5.509 0.056 5.646
metrics 4.742 0.286 5.056
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 3 WARNINGs, 4 NOTEs
See
‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/wateRmelon.Rcheck/00check.log’
for details.